Image analysis software for automatic DNA ploidy assessment of archival solid tumours.

BACKGROUND: Image cytometry has proved to provide a good alternative to flow cytometry for DNA ploidy measurement of archival tumors. However, when interactively done this technique is unable to give statistically valuable results within an acceptable time for clinical oncology. METHODS: An image cytometer was developed for fully automatic DNA ploidy quantitation, focusing efforts on speed and accuracy. Software functionalities include systematic acquisition of fields on a microscopic slide, detection, localization and sorting of nuclei, computation of the DNA content together with post-processing tools, for a deeper analysis of the DNA ploidy diagram. RESULTS: DNA ploidy analysis of archival breast carcinoma samples illustrates the accuracy of DNA ploidy measurements and the sensitivity in the detection of DNA ploidy abnormalities as a result of cell sorting. CONCLUSIONS: Fully automatic image cytometry is able to combine qualities of flow cytometry (automatic analysis of a statistically significant collection of cell nuclei) with additional advantages: sorting of unwanted events (debris, stromal and inflammatory cell nuclei) and facilities for an a posteriori control of the quality of cell selection. This method is well suited to DNA ploidy analysis of archival cancer samples.     

A user''s guide for avoiding errors in absorbance image cytometry: a review with original experimental observations

Summary The sources of errors which may occur when cytophotometric analysis is performed with video microscopy using a charged-coupled device (CCD) camera and image analysis are reviewed. The importance of these errors in practice has been tested, and ways of minimizing or avoiding them are described. Many of these sources of error are known from scanning and integrating cytophotometry; they include the use of white instead of monochromatic light, the distribution error, glare, diffraction, shading distortion, and inadequate depth of field. Sources of errors specifically linked with video microscopy or image analysis are highlighted as well; these errors include blooming, limited dynamic range of grey levels, non-linear responses of the camera, contrast transfer, photon noise, dark current, read-out noise, fixed scene noise and spatial calibration. Glare, contrast transfer, fixed scene noise, depth of field and spatial calibration seem to be the most serious sources of errors when measurements are not carried out correctly. We include a table summarizing all the errors discussed in this review and procedures for avoiding them. It can be concluded that if accurate calibration steps are performed and proper guidelines followed, image cytometry can be applied safely for quantifying amounts of chromophore per cell or per unit volume of tissue in sections, even when relatively simple and inexpensive instrumentation is being used.     

Quality assessment of confocal microscopy slide-based systems: instability.

BACKGROUND: All slide-based fluorescence cytometry detections systems basically include an excitation light source, intermediate optics, and a detection device (CCD or PMT). Occasionally, this equipment becomes unstable, generating unreliable and inferior data. METHODS: A number of tests have been devised to evaluate equipment performance and instability. The following four instability tests are described: galvanometer scanning, stage drift, correct wavelength spectral detection, and long-term laser power. RESULTS: Quality assurance tests revealed that a confocal microscope can become unstable in the following parameters, yielding inaccurate data: laser power, PMTs functionality, spectrophotometer accuracy, galvanometer scanning and laser stability, and stage drift. Long-term laser power stability has been observed to vary greatly. CONCLUSIONS: Confocal systems can become unstable in the following parameters: long-term laser power, galvanometer scanning, spectrophotometer accuracy, and stage stability. Instability in any of these parameters will affect image quality. Laser power fluctuations result from either a defective Acousto-optic tunable filter or improper heat dissipation. Spectrophotometer instability will generate unreliable spectra data, extra light reflections, and poor image quality. Galvanometer scanning instability yields poor image quality while microscope stage drift results in a sample going out of the plane of focus. With minor modifications, these tests may be applicable to other slide-based systems.     

Analytical quality--what should we be aiming for?

ISO 15189 5.5.1 "The laboratory shall use examination procedures, ... which meet the needs of the users of laboratory services and are appropriate for the examinations. Requirements for analytical quality include: understanding the analytical goal; seeking an assay that fulfills those goals; establishing your own performance with that assay; setting warning and action limits for your assay; applying quality control tools to every important step.     

阿达玛变换显微图象法测定乳腺癌DNA含量

以吖啶橙为细胞DNA荧光探针,用阿达玛(Hadamard)变换显微图象分析仪和显微荧光光度计分别测定了4例乳腺肿瘤的细胞DNA含量(倍性),并对分析结果进行了比较,二者的分析结果均与病理学诊断结论相吻合.阿达玛变换显微图象分析仪作为一种新的细胞定量分析仪器,其分析结果的准确度可与显微荧光光度计相媲美,而且阿达玛变换显微图象分析仪还具有其独特的优点,如信噪比高、具有同时分析多个细胞和同步扣除背景信号的能力等.     

Mapping cellular responses to DNA double-strand breaks using CRISPR technologies

DNA double-strand breaks (DSBs) are one of the most genotoxic DNA lesions, driving a range of pathological defects from cancers to immunodeficiencies. To combat genomic instability caused by DSBs, evolution has outfitted cells with an intricate protein network dedicated to the rapid and accurate repair of these lesions. Pioneering studies have identified and characterized many crucial repair factors in this network, while the advent of genome manipulation tools like clustered regularly interspersed short palindromic repeats (CRISPR)–CRISPR-associated protein 9 (Cas9) has reinvigorated interest in DSB repair mechanisms. This review surveys the latest methodological advances and biological insights gained by utilizing Cas9 as a precise ‘damage inducer’ for the study of DSB repair. We highlight rapidly inducible Cas9 systems that enable synchronized and efficient break induction. When combined with sequencing and genome-specific imaging approaches, inducible Cas9 systems greatly expand our capability to spatiotemporally characterize cellular responses to DSB at specific genomic coordinates, providing mechanistic insights that were previously unobtainable.     

苗期遮荫对棉花产量与品质形成的影响

为揭示棉麦两熟共生期遮荫对棉花产量与品质形成的影响。在棉花苗期利用模拟棉麦两熟共生期遮荫的方法进行了研究。结果表明,遮荫对棉铃形成的影响因果枝,果节部位而异,遮荫有利于棉株下（1-3果枝）,中（4-6果枝）,上（7-9果枝）部果枝内围（1-2果节）铃的形成,对外围（≥3果节）尤其顶部果枝（≥10果枝）外围铃形成不利,从而决定铃重也随果枝,果节部位相应地变化,但遮荫对单株平均铃重的影响畔 小,变遮荫棉花籽棉产量而论,下,中部果枝的内围铃籽棉产量高于常规棉,在上,顶部果枝则相反,各部位果枝外围铃的籽棉产量均低于常规棉,遮荫棉花内,外围铃分布为1：0.36(常规棉为1：0.58),产量分布为1：0.42(常规棉为1：0.72)。苗期遮荫对棉纤维,棉籽品质性状的影响也主要在顶部果枝和上部果枝外围铃,综合分析遮荫棉花产量与品质的形成,棉花苗期耐遮荫性品种间存在差异。在本研究中以中9418耐遮荫性最强,中棉所19和春矮早次之。     

The HOME microscope workstation. A new tool for cervical cancer screening.

The Highly Optimized Microscope Environment (HOME) is a computerized microscope design for assisting pathologists and cytotechnologists in routine clinical tasks. The prototype system consists of an IBM PC-compatible computer and a light microscope in which a built-in high-resolution computer display image is super-imposed on the optical image of the specimen. Also, an encoding stage and objective turret encoder are used to provide continuous monitoring of the stage coordinates and microscope magnification to the computer. This allows any position on the stage to be uniquely defined. Software, written in C language and running under the MS-DOS/MS-Windows environment, is controlled by means of a mouse-driven cursor. A specific application has been developed for cervical cancer screening, taking into account the needs and constraints of microscopists performing this task. Informatics tools offered by the HOME system provide them with precise flagging and relocation of objects on the slide, control of the scanning pathway, and ability to write and print the report directly through the microscope. The computer files generated by microscopic examination are stored and contain information available for quality control assessment and laboratory management.     

QCMAP: An Interactive Web‐Tool for Performance Diagnosis and Prediction of LC‐MS Systems

The increasing role played by liquid chromatography‐mass spectrometry (LC‐MS)‐based proteomics in biological discovery has led to a growing need for quality control (QC) on the LC‐MS systems. While numerous quality control tools have been developed to track the performance of LC‐MS systems based on a pre‐defined set of performance factors (e.g., mass error, retention time), the precise influence and contribution of the performance factors and their generalization property to different biological samples are not as well characterized. Here, a web‐based application (QCMAP) is developed for interactive diagnosis and prediction of the performance of LC‐MS systems across different biological sample types. Leveraging on a standardized HeLa cell sample run as QC within a multi‐user facility, predictive models are trained on a panel of commonly used performance factors to pinpoint the precise conditions to a (un)satisfactory performance in three LC‐MS systems. It is demonstrated that the learned model can be applied to predict LC‐MS system performance for brain samples generated from an independent study. By compiling these predictive models into our web‐application, QCMAP allows users to benchmark the performance of their LC‐MS systems using their own samples and identify key factors for instrument optimization. QCMAP is freely available from: http://shiny.maths.usyd.edu.au/QCMAP/ .     

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

DNA methylation is an important epigenetic modification involved in gene regulation, which can now be measured using whole-genome bisulfite sequencing. However, cost, complexity of the data, and lack of comprehensive analytical tools are major challenges that keep this technology from becoming widely applied. Here we present BSmooth, an alignment, quality control and analysis pipeline that provides accurate and precise results even with low coverage data, appropriately handling biological replicates. BSmooth is open source software, and can be downloaded from http://rafalab.jhsph.edu/bsmooth.     

The instability within: problems in current analyses of microsatellite instability

Microsatellite instability is regarded as one of the phenotypes of defective DNA mismatch repair and, consequently, as a marker of high risk for cancer. Despite numerous studies, the reported rates for positive microsatellite instability differ widely in each human malignancy. These discrepancies may relate to problems in the methods used. To establish a methodology for an accurate microsatellite instability analysis, technical requirements for a precise assay and biological conditions required for positive microsatellite instability were discussed. First, to describe microsatellite changes in detail, a sensitive detection system with linear detection characteristics and electrophoresis with standardised migration and minimised migration errors are considered to be necessary. Therefore, systems using fluorescent labelling and laser scanning are recommended. For reproducible polymerase chain reactions, it is essential to control the terminal deoxynucleotidyl transferase activity in Taq polymerase. Second, as a biological condition for positive microsatellite instability, feasible selection and combination of microsatellite markers, mutations in specific DNA mismatch repair genes and existence of monoclonal populations enriched sufficiently in a sample are essential. Finally, one possible diagnostic criterion for positive microsatellite instability is proposed, that is the existence of one of the patterns shown in the panel (see Fig. 6) at one or more loci in a set of more than five microsatellite markers.     

Finding regulatory sequences

DNA regulatory sequences control gene expression by forming DNA-protein complex with specific DNA binding protein. A major task of studies of gene regulation is to identify DNA regulatory sequences in genome-wide. Especially with the rapid pace of genome project, the function of DNA regulatory sequences becomes one of the focuses in functional genome era. Several approaches for screening and characterizing DNA regulatory sequences emerged one by one, from initial low-throughput methods to high-throughput strategies. Even though at present bioinformatics tools facilitate the process of screening regulatory fragments, the most reliable results will come from experimental test. This article highlights some experimental methods for the identification of regulatory sequences. A brief review of the history and procedures for selection methods are provided. Tendency as well as limitation and extension of these methods are also presented.     

What have we learned from finite element model studies of lumbar intervertebral discs in the past four decades?

Finite element analysis is a powerful tool routinely used to study complex biological systems. For the last four decades, the lumbar intervertebral disc has been the focus of many such investigations. To understand the disc functional biomechanics, a precise knowledge of the disc mechanical, structural and biochemical environments at the microscopic and macroscopic levels is essential. In response to this need, finite element model studies have proven themselves as reliable and robust tools when combined with in vitro and in vivo measurements.     

Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images

Background

Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of Whole Slide Images (WSI) has become a crucial issue. We present a no-reference quality assessment method that has been thoroughly tested since 2010 and is under implementation in multiple sites, both public university-hospitals and private entities. It is part of the FlexMIm R&D project which aims to improve the global workflow of digital pathology. For these uses, we have developed two programming libraries, in Java and Python, which can be integrated in various types of WSI acquisition systems, viewers and image analysis tools.

Methods

Development and testing have been carried out on a MacBook Pro i7 and on a bi-Xeon 2.7GHz server. Libraries implementing the blur assessment method have been developed in Java, Python, PHP5 and MySQL5. For web applications, JavaScript, Ajax, JSON and Sockets were also used, as well as the Google Maps API. Aperio SVS files were converted into the Google Maps format using VIPS and Openslide libraries.

Results

We designed the Java library as a Service Provider Interface (SPI), extendable by third parties. Analysis is computed in real-time (3 billion pixels per minute). Tests were made on 5000 single images, 200 NDPI WSI, 100 Aperio SVS WSI converted to the Google Maps format.

Conclusions

Applications based on our method and libraries can be used upstream, as calibration and quality control tool for the WSI acquisition systems, or as tools to reacquire tiles while the WSI is being scanned. They can also be used downstream to reacquire the complete slides that are below the quality threshold for surgical pathology analysis. WSI may also be displayed in a smarter way by sending and displaying the regions of highest quality before other regions. Such quality assessment scores could be integrated as WSI's metadata shared in clinical, research or teaching contexts, for a more efficient medical informatics workflow.

     

Tissue counter analysis of histologic sections of melanoma: influence of mask size and shape, feature selection, statistical methods and tissue preparation.

BACKGROUND: Tissue counter analysis is an image analysis tool designed for the detection of structures in complex images at the macroscopic or microscopic scale. As a basic principle, small square or circular measuring masks are randomly placed across the image and image analysis parameters are obtained for each mask. Based on learning sets, statistical classification procedures are generated which facilitate an automated classification of new data sets. OBJECTIVE: To evaluate the influence of the size and shape of the measuring masks as well as the importance of feature selection, statistical procedures and technical preparation of slides on the performance of tissue counter analysis in microscopic images. As main quality measure of the final classification procedure, the percentage of elements that were correctly classified was used. STUDY DESIGN: HE-stained slides of 25 primary cutaneous melanomas were evaluated by tissue counter analysis for the recognition of melanoma elements (section area occupied by tumour cells) in contrast to other tissue elements and background elements. Circular and square measuring masks, various subsets of image analysis features and classification and regression trees compared with linear discriminant analysis as statistical alternatives were used. The percentage of elements that were correctly classified by the various classification procedures was assessed. In order to evaluate the applicability to slides obtained from different laboratories, the best procedure was automatically applied in a test set of another 50 cases of primary melanoma derived from the same laboratory as the learning set and two test sets of 20 cases each derived from two different laboratories, and the measurements of melanoma area in these cases were compared with conventional assessment of vertical tumour thickness. RESULTS: Square measuring masks were slightly superior to circular masks, and larger masks (64 or 128 pixels in diameter) were superior to smaller masks (8 to 32 pixels in diameter). As far as the subsets of image analysis features were concerned, colour features were superior to densitometric and Haralick texture features. Statistical moments of the grey level distribution were of least significance. CART (classification and regression tree) analysis turned out to be superior to linear discriminant analysis. In the best setting, 95% of melanoma tissue elements were correctly recognized. Automated measurement of melanoma area in the independent test sets yielded a correlation of r=0.846 with vertical tumour thickness (p<0.001), similar to the relationship reported for manual measurements. The test sets obtained from different laboratories yielded comparable results. CONCLUSIONS: Large, square measuring masks, colour features and CART analysis provide a useful setting for the automated measurement of melanoma tissue in tissue counter analysis, which can also be used for slides derived from different laboratories.     

Seven-fluorochrome mouse M-FISH for high-resolution analysis of interchromosomal rearrangements

The mouse has evolved to be the primary mammalian genetic model organism. Important applications include the modeling of human cancer and cloning experiments. In both settings, a detailed analysis of the mouse genome is essential. Multicolor karyotyping technologies have emerged to be invaluable tools for the identification of mouse chromosomes and for the deciphering of complex rearrangements. With the increasing use of these multicolor technologies resolution limits are critical. However, the traditionally used probe sets, which employ 5 different fluorochromes, have significant limitations. Here, we introduce an improved labeling strategy. Using 7 fluorochromes we increased the sensitivity for the detection of small interchromosomal rearrangements (700 kb or less) to virtually 100%. Our approach should be important to unravel small interchromosomal rearrangements in mouse models for DNA repair defects and chromosomal instability.     

Predator Detection is Limited in Microhabitats with High Light Intensity: An Experiment with Brown‐Headed Cowbirds

Variations in ambient light conditions across different microhabitats can modify the detectability of predators and prey. Prey have been shown to be more visible in sunlit than in shaded patches, leading to higher predation risk and more investment in vigilance (predation risk hypothesis). Additionally, prey have been hypothesized to take longer to detect predators in sunlit compared to shaded patches because of the excess of sunlight causing glare effects (disability glare hypothesis). We tested the predictions of these two non‐mutually exclusive hypotheses in a seminatural experiment with brown‐headed cowbirds by measuring vigilance behavior and detection of a ground predator in patches under the shade of vegetation and in the open. Light intensity and achromatic contrast were higher in the sunlit patches, which could enhance glare effects, but chromatic contrast was higher in the shaded patches. Brown‐headed cowbirds took longer to show alert reactions to and flee from a ground predator in sunlit compared to shaded patches. However, the two parameters associated with perceived predation risk (vigilance prior to the predator exposure and time to resume foraging after the attack) did not differ between sunlit and shaded patches. Our findings support to a greater extent the disability glare hypothesis than the predation risk hypothesis. Overall, ambient light conditions can affect two critical components of behavioral predator–prey interactions in terrestrial habitats: detection of and escape from predators. The effects of disability glare are expected to be more pronounced in bird species with wider visual fields or without sun‐shading structures; however, species may compensate through various behaviors (e.g. avoidance of sunlit patches and changes in head orientation).     

AMarge

AMarge is a web tool for the automatic quality assessment of Affymetrix GeneChip data. It is essential to have a trustworthy set of chips in order to derive gene expression data for phenotypic analysis, and AMarge provides a complete and rigorous web-accessible tool to fulfill this need. The quality assessment steps include image plots of weights derived from a robust linear model fit of the data, a 3'/5' RNA digestion plot, and Affymetrix Microarray Suite version 5.0 (MAS 5.0) quality standard procedures. Furthermore, robust multi-array average expression values are generated in order to have a start-up expression set for the subsequent analysis. The results of the complete analysis are summarised and returned as an HTML report. AVAILABILITY: The AMarge web interface is accessible at http://nin.crg.es/cgi-binf/AMargeWeb.cgi. A mirror server is also available at http://bioinformatics.istge.it/AMarge-bin/AMargeWeb.cgi. The software implementing all these methods is part of the Bioconductor project (http://www.bioconductor.org).     

Phaedra, a protocol-driven system for analysis and validation of high-content imaging and flow cytometry

High-content screening has brought new dimensions to cellular assays by generating rich data sets that characterize cell populations in great detail and detect subtle phenotypes. To derive relevant, reliable conclusions from these complex data, it is crucial to have informatics tools supporting quality control, data reduction, and data mining. These tools must reconcile the complexity of advanced analysis methods with the user-friendliness demanded by the user community. After review of existing applications, we realized the possibility of adding innovative new analysis options. Phaedra was developed to support workflows for drug screening and target discovery, interact with several laboratory information management systems, and process data generated by a range of techniques including high-content imaging, multicolor flow cytometry, and traditional high-throughput screening assays. The application is modular and flexible, with an interface that can be tuned to specific user roles. It offers user-friendly data visualization and reduction tools for HCS but also integrates Matlab for custom image analysis and the Konstanz Information Miner (KNIME) framework for data mining. Phaedra features efficient JPEG2000 compression and full drill-down functionality from dose-response curves down to individual cells, with exclusion and annotation options, cell classification, statistical quality controls, and reporting.